fasta_util 0.2.0 → 0.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/LICENSE.txt +1 -1
- data/README.rdoc +29 -13
- data/VERSION +1 -1
- data/fasta_util.gemspec +1 -1
- metadata +2 -2
data/LICENSE.txt
CHANGED
data/README.rdoc
CHANGED
@@ -1,19 +1,35 @@
|
|
1
|
-
=
|
1
|
+
= Fasta Utility
|
2
2
|
|
3
|
-
|
3
|
+
This is a pretty simple Thor[http://github.com/wycats/thor] application for performing a number of common tasks on fasta files.
|
4
4
|
|
5
|
-
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
5
|
+
So far, supported actions are:
|
6
|
+
<tt>fasta_util lengths</tt>:: Calculates basic statistics on the lengths of the entries in the file.
|
7
|
+
<tt>fasta_util filter</tt>:: Applies a variety of filter types to the entries in a fasta file.
|
8
|
+
<tt>fasta_util clean</tt>:: Reformats each entry, wrapping long lines
|
9
|
+
<tt>fasta_util sort</tt>:: Sorts the entries in a fasta file according to length.
|
10
|
+
|
11
|
+
|
12
|
+
Detailed help on each of the options can be accessed with
|
13
|
+
|
14
|
+
fasta_util help COMMAND
|
15
|
+
|
16
|
+
eg:
|
17
|
+
|
18
|
+
$ fasta_util help filter
|
19
|
+
|
20
|
+
Usage:
|
21
|
+
fasta_util filter FILENAME [options]
|
22
|
+
|
23
|
+
Options:
|
24
|
+
-l, [--length-cutoff=N] # Only entries with length >= cutoff will be returned.
|
25
|
+
# Default: 0
|
26
|
+
-v, [--inverse-match] # Return the inverse of the match after all the other filters have been applied.
|
27
|
+
-d, [--defline-grep=DEFLINE_GREP] # A regular expression, used to search the entry's definition line.
|
28
|
+
|
29
|
+
Description:
|
30
|
+
Impose a filter or set of filters on entries in a fasta file where each sequence in the file has to pass all of the filters to be printed.
|
14
31
|
|
15
32
|
== Copyright
|
16
33
|
|
17
|
-
Copyright (c) 2011
|
18
|
-
further details.
|
34
|
+
Copyright (c) 2011 Robert Syme. MIT Licence. See LICENSE.txt for further details.
|
19
35
|
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.2.
|
1
|
+
0.2.1
|
data/fasta_util.gemspec
CHANGED
metadata
CHANGED
@@ -2,7 +2,7 @@
|
|
2
2
|
name: fasta_util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
4
|
prerelease:
|
5
|
-
version: 0.2.
|
5
|
+
version: 0.2.1
|
6
6
|
platform: ruby
|
7
7
|
authors:
|
8
8
|
- robsyme
|
@@ -126,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
126
126
|
requirements:
|
127
127
|
- - ">="
|
128
128
|
- !ruby/object:Gem::Version
|
129
|
-
hash: -
|
129
|
+
hash: -728010957941595934
|
130
130
|
segments:
|
131
131
|
- 0
|
132
132
|
version: "0"
|